No, John, if the 96 is OBDII, you can run it. 96 was a crossover year for OBDI/II. 97 was the first full year for OBDII.
JB, since you have a 97 pcm, you're totally good. The amount of tunes you're limited to is only your willingness you possibly fry your PCM. Repeatedly writing and rewriting data to the PCMs, it stresses them and in some cases can cause them to not be writable anymore. That is on the PCM side
On the tuner side, it doesn't care how many tunes you change over, however, SCTs are (or have been, anyway) limited to 3 "Return to Stock" settings.